Life science discoveries large and small rely on biological collections

by Kyria Boundy-Mills

Curator, Phaff Yeast Culture Collection, UC Davis

A recent high-profile scientific publication (Dash et al. 2019) caught fire in the popular press: Scientists at the University of Nebraska and Temple University found a way to eliminate HIV virus from infected mice. Their protocol may lead to a cure for HIV infection in people. Wow!! That’s big! 

Because I am a yeast collection curator, when I read scientific publications, I pay attention to what (and how many) repositories provided biological materials. I mentally give one point for each repository tapped. For example, a recent study about a bacterial plant pathogen that infests citrus used bacteria from the USDA-ARS and state repositories, insect vectors from the University of California-ANR, and citrus seeds from a program at UC Riverside. Four repositories, four points.

Reading Dash et al. 2019 was like hitting the jackpot: 6 sources in one paper! The biological materials listed in the Materials and Methods section include:

1. ·      Mice from Jackson Laboratories
2. ·      Human cell lines from ATCC and the Aids Reagent Program of NIAID
3. ·      HIV-1 virus from the NIH Aids Reagent Program
4. ·      Vectors and plasmids from Addgene
5. ·      AAV-9 virus from Vigene Biosciences Inc. (the virus that delivers the CRISPR-Cas9 treatment to the mouse genome to excise the HIV-1)
6. ·      Antibodies from BD Biosciences and BD Parmingen

MMRRC mouse line from the UC Davis Mouse Biology Program, 

photo by M. Valenzuela, provided by Renee Araiza 

But wait, there’s more! Many other items used in this study such as enzymes, CRISPR-Cas9, and antibiotics may also be linked to biological collections. The Taq polymerase enzyme used in PCR and DNA sequencing traces its origin to a strain of Thermus aquaticus obtained from the American Type Culture Collection (ATCC). When my thesis advisor Dennis Livingston was a student, he had to order specific bacteria from collections and isolate his own restriction enzymes for his experiments. Thank goodness times have changed, we can just order these materials from catalogs now. But the enzymes and other essential items we use today trace their origin to living organisms, many of which were preserved in and obtained from culture collections. 

Moral of the story: Take a moment to appreciate the many repositories that contribute to your life science discoveries.

Reference: Dash, P.K., et al., Sequential LASER ART and CRISPR treatments eliminate HIV-1 in a subset of infected humanized mice. Nature communications, 2019. 10(1): p. 1-20.

The less exciting details, for the benefit of you list-o-philes:

Materials cited in the Materials and Methods section that came from biological collections and biological supplier companies:

·       TZM-bl reporter cell line (AIDS Reagent Program, Division of AIDS, NIAID, NIH, Bethesda, MD) 

·       HEK-293T cells (the American Type Culture Collection (ATCC), Manassas, VA)

·       Jurkat (Clone E6–1, TIB-152™) cells were purchased from ATCC

·       [HIV-1 Virus?] HIV-1NL4–3 

·       Vector pX601-AAVCMV: NLS-saCas9-NLS-3xHA-bGHpA;U6::BsaI-sgRNA (a gift from Feng Zhang via Addgene) (61591; Addgene).

·       pKLV-U6gRNA(Bbs1)-PGKpuro2ABFP (Addgene catalog #50946)

·       AAV-9 serotype (Vigene Biosciences Inc., Milton Park Abingdon, UK).

·       Mice NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice were obtained from the Jackson Laboratories, Bar Harbor, ME

·       antibodies (all from BD Biosciences, San Jose, CA); Antibodies and isotype controls were obtained from BD Pharmingen, San Diego, CA,

Materials that came indirectly from biological organisms and/or collections:

·      Reagents such as ciprofloxacin, gentamicin, interleukin-2, puromycin

·      Plasmids such as pNL4–3-EGFP-P2A-Nef plasmid

·      DNA sequences used for CRISPR-Cas9; HIV-1 genome database; human genome

·      The Taq polymerase used in PCR, qPCR and Sanger and next generation DNA sequencing ultimately originated from Thermus aquaticus ATCC [number]

·      Restriction enzymes Bsa1, EcoRI, KpnI

·      Other enzymes including DNase I, proteinase K, 

·      Vectors such as AAV-CMV-saCas9 vector 

·      In-Fusion HD Cloning Kit (Clontech, Mountain View, CA)